Hello. First, make sure you have the latest build of the component. Two, make sure you watch our custom fields video tutorial as it is 99% chance that you don't have it setup correctly
Where you are probably messed up is the selection limits. For each value option for the checkboxes, you must have a selection limit. "0" would represent unlimited. This limit means how many times can that option be chosen during the lifetime of that event... like a capacity setting for each checkbox. If it doesn't matter, give each one a 0. So if you have checkboxes like this:
Box One|Box Two|Box Three|Box Four
Your selection limits would look like this:
0|0|0|0
That would be for unlimited. Enter a number for each if you want to put a limit on how many times it can be chosen. Thanks.